Solved. **Someone** had decided to amend one of the templates we use to create the profiles and had unticked the box that allows the adminsitrator tool to be shown! They decided to keep this information to themselves! The template they created has now been removed and all other profiles created with it modified to allow the administrator tool!
Also. If the Administrator Tool has been disabled we have found a way to re-enable it by editing the ini file.
The file is ItSttngs.ini
It is located in: C:\Documents and Settings\All Users\Application Data\Intel\Wireless\Settings
The value to change is: ITAdminTool
To enable Administrator Tool: ITAdminTool=0
To disable Administrator Tool: ITAdminTool=1